Skip to content

Commit ea722c2

Browse files
andreasprlicandreasprlic
committed
Merge branch 'master' of github.com:biojava/biojava
* 'master' of github.com:biojava/biojava: (47 commits) [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-5.0.0-alpha4 [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-4.2.2 [maven-release-plugin] rollback the release of biojava-4.2.2 [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-4.2.2 [maven-release-plugin] rollback the release of biojava-4.2.2 [maven-release-plugin]prepare release biojava-4.2.2 enabling useReleaseProfile by default now. [maven-release-plugin] rollback the release of biojava-4.2.2 [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-4.2.2 squid:S2063 - Comparators should be Serializable trying to get jenkins to auto-release to oss sonatype trying to get jenkins to auto-release to oss sonatype Empty ' ' inscode or altloc is now a null byte Updating ptm list. A couple of SymmetryGUI improvements Solve warnings ... # Conflicts: # biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml
2 parents 80dd887 + 34b2bf9 commit ea722c2

File tree

40 files changed

+1371
-642
lines changed

40 files changed

+1371
-642
lines changed

‎biojava-alignment/pom.xml‎

Lines changed: 30 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -26,16 +26,16 @@
2626

2727
<!-- Excluding demo package is required for avoiding namespace clashes
2828
(demo package is in all modules) for signing the jar. See issue #387 -->
29-
<plugin>
30-
<groupId>org.apache.maven.plugins</groupId>
31-
<artifactId>maven-jar-plugin</artifactId>
32-
<configuration>
33-
<excludes>
34-
<exclude>demo/**</exclude>
35-
</excludes>
36-
</configuration>
37-
</plugin>
38-
29+
<plugin>
30+
<groupId>org.apache.maven.plugins</groupId>
31+
<artifactId>maven-jar-plugin</artifactId>
32+
<configuration>
33+
<excludes>
34+
<exclude>demo/**</exclude>
35+
</excludes>
36+
</configuration>
37+
</plugin>
38+
3939
</plugins>
4040
</build>
4141
<dependencies>
@@ -57,26 +57,26 @@
5757
<!-- logging dependencies (managed by parent pom, don't set versions or
5858
scopes here) -->
5959
<dependency>
60-
<groupId>org.slf4j</groupId>
61-
<artifactId>slf4j-api</artifactId>
62-
</dependency>
63-
<!-- binding for log4j2, scope=runTime set in parent pom -->
64-
<dependency>
65-
<groupId>org.apache.logging.log4j</groupId>
66-
<artifactId>log4j-slf4j-impl</artifactId>
67-
</dependency>
68-
<dependency>
69-
<groupId>org.apache.logging.log4j</groupId>
70-
<artifactId>log4j-api</artifactId>
71-
</dependency>
72-
<dependency>
73-
<groupId>org.apache.logging.log4j</groupId>
74-
<artifactId>log4j-core</artifactId>
75-
</dependency>
76-
<dependency>
77-
<groupId>org.biojava</groupId>
78-
<artifactId>biojava-phylo</artifactId>
60+
<groupId>org.slf4j</groupId>
61+
<artifactId>slf4j-api</artifactId>
62+
</dependency>
63+
<!-- binding for log4j2, scope=runTime set in parent pom -->
64+
<dependency>
65+
<groupId>org.apache.logging.log4j</groupId>
66+
<artifactId>log4j-slf4j-impl</artifactId>
67+
</dependency>
68+
<dependency>
69+
<groupId>org.apache.logging.log4j</groupId>
70+
<artifactId>log4j-api</artifactId>
71+
</dependency>
72+
<dependency>
73+
<groupId>org.apache.logging.log4j</groupId>
74+
<artifactId>log4j-core</artifactId>
75+
</dependency>
76+
<dependency>
77+
<groupId>org.biojava</groupId>
78+
<artifactId>biojava-phylo</artifactId>
7979
<version>5.0.0-SNAPSHOT</version>
80-
</dependency>
80+
</dependency>
8181
</dependencies>
8282
</project>

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,7 @@
2525

2626
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
2727

28+
import java.io.Serializable;
2829
import java.util.ArrayList;
2930
import java.util.Collections;
3031
import java.util.Comparator;
@@ -207,7 +208,9 @@ public Anchor(int queryIndex, int targetIndex) {
207208
this.queryIndex = queryIndex;
208209
this.targetIndex = targetIndex;
209210
}
210-
public static class QueryIndexComparator implements Comparator<Anchor> {
211+
public static class QueryIndexComparator implements Comparator<Anchor>, Serializable {
212+
private static final long serialVersionUID = 1;
213+
211214
@Override
212215
public int compare(Anchor o1, Anchor o2) {
213216
return o1.getQueryIndex() - o2.getQueryIndex();

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,11 +23,13 @@
2323

2424
package org.biojava.nbio.core.sequence;
2525

26+
import java.io.Serializable;
2627
import java.util.Comparator;
2728

2829

2930

30-
public class CDSComparator implements Comparator<CDSSequence>{
31+
public class CDSComparator implements Comparator<CDSSequence>, Serializable{
32+
private static final long serialVersionUID = 1;
3133

3234
/**
3335
* Used to sort two CDSSequences where Negative Strand makes it tough

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
2323

2424
package org.biojava.nbio.core.sequence;
2525

26+
import java.io.Serializable;
2627
import java.util.Comparator;
2728

2829

@@ -31,8 +32,8 @@
3132
* where a negative stranded gene should go the other direction. Need to think about this?
3233
* @author Scooter Willis <willishf at gmail dot com>
3334
*/
34-
public class ExonComparator implements Comparator<ExonSequence>{
35-
35+
public class ExonComparator implements Comparator<ExonSequence>, Serializable{
36+
private static final long serialVersionUID = 1;
3637

3738
@Override
3839
public int compare(ExonSequence o1, ExonSequence o2) {

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,14 +24,15 @@
2424

2525
import org.biojava.nbio.core.sequence.template.AbstractSequence;
2626

27+
import java.io.Serializable;
2728
import java.util.Comparator;
2829

2930
/**
3031
* Used to sort sequences
3132
* @author Scooter Willis <willishf at gmail dot com>
3233
*/
33-
public class SequenceComparator implements Comparator<AbstractSequence<?>>{
34-
34+
public class SequenceComparator implements Comparator<AbstractSequence<?>>, Serializable{
35+
private static final long serialVersionUID = 1;
3536

3637
@Override
3738
public int compare(AbstractSequence<?> o1, AbstractSequence<?> o2) {

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -228,7 +228,7 @@ private List<Location> parseLocationString(String string, int versus) throws Par
228228

229229
String accession = m.group(1);
230230
Strand s = versus == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
231-
int start = new Integer(m.group(3));
231+
int start = Integer.parseInt(m.group(3));
232232
int end = m.group(6) == null ? start : new Integer(m.group(6));
233233

234234
if (featureGlobalStart > start) {

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222

2323
import org.biojava.nbio.core.sequence.DNASequence;
2424

25+
import java.io.Serializable;
2526
import java.util.*;
2627
import java.util.Map.Entry;
2728

@@ -467,7 +468,8 @@ public String toString() {
467468
/**
468469
* used by sort routine
469470
*/
470-
private class FeatureComparator implements Comparator<FeatureI> {
471+
private class FeatureComparator implements Comparator<FeatureI>, Serializable {
472+
private static final long serialVersionUID = 1;
471473

472474
@Override
473475
public int compare(FeatureI a, FeatureI b) {

‎biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,7 @@
1919
*
2020
* Created on Jun 8, 2010
2121
* Author: Jianjiong Gao
22+
* Author: Peter W. Rose
2223
*
2324
*/
2425

‎biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/InputParameters.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -105,10 +105,10 @@ ResultLayout parseFormat(String format) {
105105
return ResultLayout.VERTICAL;
106106
}
107107
format = format.trim().substring(InputParameters.formatKey.length());
108-
if (format.toUpperCase().equals("V")) {
108+
if ("V".equalsIgnoreCase(format)) {
109109
return ResultLayout.VERTICAL;
110110
}
111-
if (format.toUpperCase().equals("H")) {
111+
if ("H".equalsIgnoreCase(format)) {
112112
return ResultLayout.HORIZONTAL;
113113
}
114114
throw new IllegalArgumentException("Unrecognised format: '" + format

‎biojava-structure-gui/pom.xml‎

Lines changed: 82 additions & 83 deletions
Original file line numberDiff line numberDiff line change
@@ -1,95 +1,94 @@
11
<?xml version="1.0" encoding="UTF-8"?>
2-
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
3-
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
4-
<parent>
5-
<artifactId>biojava</artifactId>
6-
<groupId>org.biojava</groupId>
2+
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
3+
<parent>
4+
<artifactId>biojava</artifactId>
5+
<groupId>org.biojava</groupId>
76
<version>5.0.0-SNAPSHOT</version>
8-
</parent>
9-
<modelVersion>4.0.0</modelVersion>
10-
<artifactId>biojava-structure-gui</artifactId>
11-
<name>biojava-structure-gui</name>
12-
<url>http://www.biojava.org</url>
13-
<licenses>
14-
<license>
15-
<name>GNU LGPL v2</name>
16-
<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
17-
<distribution>repo</distribution>
18-
</license>
19-
</licenses>
7+
</parent>
8+
<modelVersion>4.0.0</modelVersion>
9+
<artifactId>biojava-structure-gui</artifactId>
10+
<name>biojava-structure-gui</name>
11+
<url>http://www.biojava.org</url>
12+
<licenses>
13+
<license>
14+
<name>GNU LGPL v2</name>
15+
<url>http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt</url>
16+
<distribution>repo</distribution>
17+
</license>
18+
</licenses>
2019

21-
<dependencies>
22-
<dependency>
23-
<groupId>junit</groupId>
24-
<artifactId>junit</artifactId>
25-
<scope>test</scope>
26-
</dependency>
20+
<dependencies>
21+
<dependency>
22+
<groupId>junit</groupId>
23+
<artifactId>junit</artifactId>
24+
<scope>test</scope>
25+
</dependency>
2726

28-
<dependency>
29-
<groupId>org.biojava</groupId>
30-
<artifactId>biojava-structure</artifactId>
27+
<dependency>
28+
<groupId>org.biojava</groupId>
29+
<artifactId>biojava-structure</artifactId>
3130
<version>5.0.0-SNAPSHOT</version>
32-
<scope>compile</scope>
33-
</dependency>
34-
<dependency>
35-
<groupId>org.biojava</groupId>
36-
<artifactId>biojava-core</artifactId>
31+
<scope>compile</scope>
32+
</dependency>
33+
<dependency>
34+
<groupId>org.biojava</groupId>
35+
<artifactId>biojava-core</artifactId>
3736
<version>5.0.0-SNAPSHOT</version>
38-
<scope>compile</scope>
39-
</dependency>
37+
<scope>compile</scope>
38+
</dependency>
4039

41-
<!-- Include jMol LAST, as it shades in several unwanted dependencies,
42-
notably commons-cli:1.1 -->
43-
<dependency>
44-
<groupId>net.sourceforge.jmol</groupId>
45-
<artifactId>jmol</artifactId>
46-
<version>13.0.14</version>
47-
</dependency>
48-
<!-- logging dependencies (managed by parent pom, don't set versions or
49-
scopes here) -->
50-
<dependency>
51-
<groupId>org.slf4j</groupId>
52-
<artifactId>slf4j-api</artifactId>
53-
</dependency>
54-
<!-- binding for log4j2, scope=runTime set in parent pom -->
55-
<dependency>
56-
<groupId>org.apache.logging.log4j</groupId>
57-
<artifactId>log4j-slf4j-impl</artifactId>
58-
</dependency>
59-
<dependency>
60-
<groupId>org.apache.logging.log4j</groupId>
61-
<artifactId>log4j-api</artifactId>
62-
</dependency>
63-
<dependency>
64-
<groupId>org.apache.logging.log4j</groupId>
65-
<artifactId>log4j-core</artifactId>
66-
</dependency>
67-
<dependency>
68-
<groupId>org.biojava</groupId>
69-
<artifactId>jcolorbrewer</artifactId>
70-
<version>5.2</version>
71-
</dependency>
72-
</dependencies>
73-
<properties>
74-
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
75-
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
76-
</properties>
77-
<build>
78-
<plugins>
40+
<!-- Include jMol LAST, as it shades in several unwanted dependencies,
41+
notably commons-cli:1.1 -->
42+
<dependency>
43+
<groupId>net.sourceforge.jmol</groupId>
44+
<artifactId>jmol</artifactId>
45+
<version>13.0.14</version>
46+
</dependency>
47+
<!-- logging dependencies (managed by parent pom, don't set versions or
48+
scopes here) -->
49+
<dependency>
50+
<groupId>org.slf4j</groupId>
51+
<artifactId>slf4j-api</artifactId>
52+
</dependency>
53+
<!-- binding for log4j2, scope=runTime set in parent pom -->
54+
<dependency>
55+
<groupId>org.apache.logging.log4j</groupId>
56+
<artifactId>log4j-slf4j-impl</artifactId>
57+
</dependency>
58+
<dependency>
59+
<groupId>org.apache.logging.log4j</groupId>
60+
<artifactId>log4j-api</artifactId>
61+
</dependency>
62+
<dependency>
63+
<groupId>org.apache.logging.log4j</groupId>
64+
<artifactId>log4j-core</artifactId>
65+
</dependency>
66+
<dependency>
67+
<groupId>org.biojava</groupId>
68+
<artifactId>jcolorbrewer</artifactId>
69+
<version>5.2</version>
70+
</dependency>
71+
</dependencies>
72+
<properties>
73+
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
74+
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
75+
</properties>
76+
<build>
77+
<plugins>
7978

8079
<!-- Excluding demo package is required for avoiding namespace clashes
8180
(demo package is in all modules) for signing the jar. See issue #387 -->
82-
<plugin>
83-
<groupId>org.apache.maven.plugins</groupId>
84-
<artifactId>maven-jar-plugin</artifactId>
85-
<configuration>
86-
<excludes>
87-
<exclude>demo/**</exclude>
88-
</excludes>
89-
</configuration>
90-
</plugin>
91-
92-
</plugins>
93-
</build>
81+
<plugin>
82+
<groupId>org.apache.maven.plugins</groupId>
83+
<artifactId>maven-jar-plugin</artifactId>
84+
<configuration>
85+
<excludes>
86+
<exclude>demo/**</exclude>
87+
</excludes>
88+
</configuration>
89+
</plugin>
90+
91+
</plugins>
92+
</build>
9493

9594
</project>

0 commit comments

Comments
 (0)